9 research outputs found

    A Predictive Model of the Oxygen and Heme Regulatory Network in Yeast

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    Deciphering gene regulatory mechanisms through the analysis of high-throughput expression data is a challenging computational problem. Previous computational studies have used large expression datasets in order to resolve fine patterns of coexpression, producing clusters or modules of potentially coregulated genes. These methods typically examine promoter sequence information, such as DNA motifs or transcription factor occupancy data, in a separate step after clustering. We needed an alternative and more integrative approach to study the oxygen regulatory network in Saccharomyces cerevisiae using a small dataset of perturbation experiments. Mechanisms of oxygen sensing and regulation underlie many physiological and pathological processes, and only a handful of oxygen regulators have been identified in previous studies. We used a new machine learning algorithm called MEDUSA to uncover detailed information about the oxygen regulatory network using genome-wide expression changes in response to perturbations in the levels of oxygen, heme, Hap1, and Co2+. MEDUSA integrates mRNA expression, promoter sequence, and ChIP-chip occupancy data to learn a model that accurately predicts the differential expression of target genes in held-out data. We used a novel margin-based score to extract significant condition-specific regulators and assemble a global map of the oxygen sensing and regulatory network. This network includes both known oxygen and heme regulators, such as Hap1, Mga2, Hap4, and Upc2, as well as many new candidate regulators. MEDUSA also identified many DNA motifs that are consistent with previous experimentally identified transcription factor binding sites. Because MEDUSA's regulatory program associates regulators to target genes through their promoter sequences, we directly tested the predicted regulators for OLE1, a gene specifically induced under hypoxia, by experimental analysis of the activity of its promoter. In each case, deletion of the candidate regulator resulted in the predicted effect on promoter activity, confirming that several novel regulators identified by MEDUSA are indeed involved in oxygen regulation. MEDUSA can reveal important information from a small dataset and generate testable hypotheses for further experimental analysis. Supplemental data are included

    Optimal dispatch of hybrid energy islanded microgrid considering V2G under TOU tariffs

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    In order to achieve a prospective economic effect of renewable energy generations and vehicle to grid (V2G), this paper proposes an optimal dispatch method of wind-PV-battery microgrid considering V2G under time-of-use (TOU) tariffs for those isolated communities in remote islands and mountainous areas. A cooperative dispatch strategy and an optimal dispatch model are both presented for the total operation cost minimization and higher utilization of renewable energy generation. Finally, the simulation results show that the proposed method is effective and feasible

    Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance

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    Hypoxia is a widely occurring condition experienced by diverse organisms under numerous physiological and disease conditions. To probe the molecular mechanisms underlying hypoxia responses and tolerance, we performed a genome-wide screen to identify mutants with enhanced hypoxia tolerance in the model eukaryote, the yeast Saccharomyces cerevisiae. Yeast provides an excellent model for genomic and proteomic studies of hypoxia. We identified five genes whose deletion significantly enhanced hypoxia tolerance. They are RAI1, NSR1, BUD21, RPL20A, and RSM22, all of which encode functions involved in ribosome biogenesis. Further analysis of the deletion mutants showed that they minimized hypoxia-induced changes in polyribosome profiles and protein synthesis. Strikingly, proteomic analysis by using the iTRAQ profiling technology showed that a substantially fewer number of proteins were changed in response to hypoxia in the deletion mutants, compared with the parent strain. Computational analysis of the iTRAQ data indicated that the activities of a group of regulators were regulated by hypoxia in the wild-type parent cells, but such regulation appeared to be diminished in the deletion strains. These results show that the deletion of one of the genes involved in ribosome biogenesis leads to the reversal of hypoxia-induced changes in gene expression and related regulators. They suggest that modifying ribosomal function is an effective mechanism to minimize hypoxia-induced specific protein changes and to confer hypoxia tolerance. These results may have broad implications in understanding hypoxia responses and tolerance in diverse eukaryotes ranging from yeast to humans

    Enhanced Hydrogen Detection Based on Mg-Doped InN Epilayer

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    It is a fact that surface electron accumulation layer with sheet electron density in the magnitude of ~1013 cm−2 on InN, either as-grown or Mg-doped, makes InN an excellent candidate for sensing application. In this paper, the response of hydrogen sensors based on Mg-doped InN films (InN:Mg) grown by molecular beam epitaxy has been investigated. The sensor exhibits a resistance variation ratio of 16.8% with response/recovery times of less than 2 min under exposure to 2000 ppm H2/air at 125 °C, which is 60% higher in the magnitude of response than the one based on the as-grown InN film. Hall-effect measurement shows that the InN:Mg with suitable Mg doping level exhibits larger sheet resistance, which accords with buried p-type conduction in the InN bulk. This work shows the advantage of InN:Mg and signifies its potential for sensing application

    Exciton emission of quasi-2D InGaN in GaN matrix grown by molecular beam epitaxy

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    We investigate the emission from confined excitons in the structure of a single-monolayer-thick quasi-two-dimensional (quasi-2D) InxGa1-xN layer inserted in GaN matrix. This quasi-2D InGaN layer was successfully achieved by molecular beam epitaxy (MBE), and an excellent in-plane uniformity in this layer was confirmed by cathodoluminescence mapping study. The carrier dynamics have also been investigated by time-resolved and excitation-power-dependent photoluminescence, proving that the recombination occurs via confined excitons within the ultrathin quasi-2D InGaN layer even at high temperature up to similar to 220 K due to the enhanced exciton binding energy. This work indicates that such structure affords an interesting opportunity for developing high-performance photonic devices.National Key Research and Development Program of China [2016YFB0400100]; National Natural Science Foundation of China [61225019, 61376060, 61428401, 61521004]; Science Challenge Project [JCKY2016212A503]; NSAF [U1630109]; CAEP Microsystem and THz Science and Technology Foundation [CAEPMT201507]; Open Fund of the State Key Laboratory on Integrated OptoelectronicsSCI(E)ARTICLE
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